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Shai Carmi

@shaicarmi.bsky.social
930 followers 225 following 480 posts

Associate professor at the Hebrew University of Jerusalem. Statistical, population, and medical genetics; preimplantation genetic testing. Views my own. scarmilab.org

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Reposted by Shai Carmi
Pol Solé Navais @polsolenavais.bsky.social · 02/10/2026
📣📣📣 We are hiring a PhD student in reproductive genetics! The candidate will join our computational efforts to map the genetics behind pregnancy loss from both the fetal and maternal sides, working with a large pregnancy loss cohort and a new sequencing effort that we are launching. #PhD 1/3
web103.reachmee.com
Doctoral student in Medical Science - reproductive genetics and bioinformatics
Doctoral position in Medical Science Project title:  The role of aneuploidies and fetal and maternal genetics
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Shai Carmi @shaicarmi.bsky.social · 02/10/2026
It is now October 2026. Since June 2025 (16 months), my kids have had only 7 months of normal school schedule. Since 2019 we have not had a single normal year. I am running on fumes.
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Shai Carmi @shaicarmi.bsky.social · 23/09/2026
Just received from a journal an entirely AI-generated peer review. I knew the day would come. Academia is doomed.
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Shai Carmi @shaicarmi.bsky.social · 22/09/2026
Given the recent decline of social media for high quality science discussions, I have recently moved most of my activity into this Slack group, dedicated to population genetics and genetic genealogy. Everyone is welcome to join: join.slack.com/t/geneticgen...
join.slack.com
Join Genetic genealogy science on Slack
Slack is a new way to communicate with your team. It’s faster, better organized, and more secure than email.
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Shai Carmi @shaicarmi.bsky.social · 21/09/2026
Interesting!
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Shai Carmi @shaicarmi.bsky.social · 20/09/2026
Academic Age Acceleration: Your age minus your h-index (Mine's positive unfortunately)
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Reposted by Shai Carmi
alex ioannidis @alexgioannidis.bsky.social · 17/09/2026
Fst is a key genetic differentiation metric, but it emphasizes common variants over rare. In IEEE ICASSP out now lab member Margarita Geleta introduces Fq, which can be tuned across the allele freq spectrum. Fst & Shannon differentiation fall out of it as special cases. arxiv.org/abs/2511.03063
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 15/09/2026
Estimating de novo mutation rates using parent-offspring pairs www.biorxiv.org/content/10.64898/20…
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bioRxiv Genomics @biorxiv-genomic.bsky.social · 12/09/2026
Sparse Linear Algebra Accelerates Genotype Representation Graph Computation at Biobank Scale www.biorxiv.org/content/10.64898/20…
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Rémy Furrer @remyfurrer.bsky.social · 10/09/2026
What are IVF doctors’ views on polygenic embryo screening (PES/PGT-P), and what criteria shape their decisions? New survey results from 152 clinicians. @gimjournal.bsky.social @shaicarmi.bsky.social @toddlencz.bsky.social www.gimjournal.org/article/S109...
gimjournal.org
Decision-making criteria in polygenic embryo screening: A survey of reproductive medicine physicians
Polygenic embryo screening (PES) examines embryos for their genetic likelihood of developing complex conditions and traits. The commercialization of PES places reproductive endocrinologists and infert...
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Reposted by Shai Carmi
Rémy Furrer @remyfurrer.bsky.social · 03/09/2026
Link to letter: www.economist.com/letters/2026... Link to study: jamanetwork.com/journals/jam...
economist.com
The opposition of scientific research on animals | Sep 5th 2026 Edition
Also this week, humanitarian aid, polygenic embryo selection, Dolly Parton, relaxing holidays, Lake Ontario
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alex ioannidis @alexgioannidis.bsky.social · 01/09/2026
Gnomix is published! www.nature.com/articles/s41... Still the most accurate & fastest local ancestry inference (LAI) method, bests Flare and others (RecombMix & Orchestra) released since our preprint. Easy to use, github.com/AI-sandbox/g... Use it with our toolkit, snputils.org
nature.com
Scalable high resolution ancestry deconvolution for genomic data - Nature Communications
The authors present Gnomix, a local ancestry framework that delivers leading accuracy across diverse admixed datasets on both whole-genome and array data with high efficiency, together with Gnofix, it...
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Erkin Alaçamlı @masterolojist.bsky.social · 20/08/2026
Our new preprint is out: www.biorxiv.org/content/10.6... (1/n)
biorxiv.org
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Shai Carmi @shaicarmi.bsky.social · 12/08/2026
New preprint! Investigative genetic genealogy has revolutionized forensic identification, with hundreds of cases solved to date. But for any given new case, how likely is genetic genealogy to succeed? We used a whole-country genealogy to find out! 1/10 www.biorxiv.org/content/10.6...
biorxiv.org
Forensic investigative genetic genealogy match rate estimated from a nation-wide population register
Forensic investigative genetic genealogy (FIGG) is a revolutionary method in forensic genetics, whereby genetic relatives of an unknown target person are detected in direct-to-consumer genomic databas...
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Shai Carmi @shaicarmi.bsky.social · 12/08/2026
New preprint! Investigative genetic genealogy has revolutionized forensic identification, with hundreds of cases solved to date. But for any given new case, how likely is genetic genealogy to succeed? We used a whole-country genealogy to find out! 1/10 www.biorxiv.org/content/10.6...
biorxiv.org
Forensic investigative genetic genealogy match rate estimated from a nation-wide population register
Forensic investigative genetic genealogy (FIGG) is a revolutionary method in forensic genetics, whereby genetic relatives of an unknown target person are detected in direct-to-consumer genomic databas...
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Reposted by Shai Carmi
Mike Inouye @mikeinouye.bsky.social · 02/08/2026
If you're looking to do a postdoc or a PhD, check out our exemplar publications and feel free to get in touch: www.inouyelab.org/home/publica...
inouyelab.org
Inouye Lab - Publications
Google Scholar Inouye Lab authors * denotes equal contribution
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alex ioannidis @alexgioannidis.bsky.social · 30/07/2026
Just got our @genomeresearch.bsky.social article by Margarita Geleta. 📬 I love hard copies...still here's a link genome.cshlp.org/content/36/2... Rita's article was a tour de force of genomic uses for the autoencoder architecture: compression, dim reduction, ancestry, synthetic genomes.
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Sini Nagpal @nagpalsini.bsky.social · 24/07/2026
Excited to share our work on "Pervasive interactions between exposures and polygenic risk can inform more effective clinical and behavioral interventions" @genomestake.bsky.social @natgenet.nature.com - www.nature.com/articles/s41...
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Nicola Pirastu @npirastu.bsky.social · 25/07/2026
We’re looking for a Statistical Geneticist to join our team at @humantechnopole.bsky.social. The role offers the opportunity to work across a wide range of projects, supporting research groups throughout Human Technopole while developing and implementing new statistical methods tinyurl.com/44uyt8u2
tinyurl.com
Statistical Geneticist
Statistical Geneticist
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loic-yengo.bsky.social @loic-yengo.bsky.social · 21/07/2026
Come and join our dream team! We’re recruiting a PhD candidate with a strong background in statistics, machine learning and (human) genetics to work at the interface of biological sequence foundational models and scores polygenic score methods.
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Padraig Dixon @padraigdixon.bsky.social · 16/07/2026
New preprint: genetic variation and healthcare spending Across ~1.43M people, we identify hundreds of cost-associated variants, strong HLA signals, and higher costs among carriers of rare pathogenic variants in genes including BRCA1/2 and APC. www.medrxiv.org/content/10.6...
medrxiv.org
Quantifying the contribution of genetic variation to healthcare expenditure across diverse healthcare systems
Healthcare systems must balance rising costs with the delivery of effective care, yet the factors underlying large inter-individual differences in healthcare expenditure remain incompletely understood...
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alex ioannidis @alexgioannidis.bsky.social · 16/07/2026
Scaling genetic clustering (ADMIXTURE/STRUCTURE-style unsupervised clustering) is now easy. Out in Bioinformatics, our ADAMIXTURE method clusters all of UK Biobank (500k genomes) in just over a hour with likelihoods as good as ADMIXTURE, which would take weeks. doi.org/10.1093/bioi...
doi.org
ADAMIXTURE: adaptive first-order optimization for biobank-scale genetic clustering
AbstractMotivation. Estimating genetic clusters from sequencing data is a fundamental task in population and medical genetics, enabling demographic inferen
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Sini Nagpal @nagpalsini.bsky.social · 15/07/2026
Excited to share 2 important milestones in my academic journey- Our work on “Pervasive interactions between exposures & polygenic risk can inform more effective clinical & behavioral interventions,” showing PGSxC interactions & their utility, is out in #NatureGenetics @genomestake.bsky.social
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Shai Carmi @shaicarmi.bsky.social · 03/07/2026
A meta-science thought. There are >11k papers on PubMed on polygenic scores. It's a huge waste of resources. It's mostly one question that matters. When reporting to people either their real PRS or a random PRS, do people in the real PRS group have better health outcomes years later?
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Kristján Moore (Kris)🔸 @kristjanmoore.bsky.social · 02/07/2026
Pre-print on the impacts of the second plague pandemic and concurrent historical processes in 529 human genomes (mean 8.8x) from @ucph.bsky.social, Amgen/deCODE genetics, and many collaborators. We'd be grateful for any feedback before publication, so please share!
PCA of ancient individuals included in our study. We observe mostly northern European ancestry with three notable outliers.Selection scan in pre-Black Death versus post-Black Death samples showing no significant results.
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Shai Carmi @shaicarmi.bsky.social · 02/07/2026
The UK Biobank being inaccessible for half a year is annoying but also a great natural experiment. I'm wondering if in 3-4 years scientists could see the impact. Could teach us a lot about the scientific process and the value of biobanks.
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Arev P. Sümer @arevsumer.bsky.social · 27/06/2026
All talks are now available including mine: www.youtube.com/watch?v=zZmF... Luckily the video became online on the same day as the paper I talked about at the end of my talk "confidentially" 😅
youtube.com
Du Paléolithique moyen au Paléolithique supérieur... (4) - Jean-Jacques Hublin (2025-2026)
YouTube video by Sciences de la vie - Collège de France
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Ludvig Daae Bjørndal @ludvigdb.bsky.social · 23/06/2026
Family history has been recognised as a risk factor for psychiatric disorders since the late 18th century. In this new preprint, we leverage family history of psych and neurodev diagnoses to estimate family-genetic risk scores (PA-FGRSs) in the Norwegian population🧵 doi.org/10.31234/osf...
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bioRxiv Genetics @biorxiv-genetic.bsky.social · 19/06/2026
From Nuisance to Signal: Leveraging Close Relatives in Biobank-Scale Demographic Inference www.biorxiv.org/content/10.64898/20…
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Shai Carmi @shaicarmi.bsky.social · 16/06/2026
Accepted a review request two weeks ago for a Springer journal. Reminder emails on days 6, 9, 13, and again on day 13. Spent a day reading and preparing the review. On day 14, just before sending out the review, received a message that my review is no longer needed. Why do we agree to this???
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Shai Carmi @shaicarmi.bsky.social · 12/06/2026
Nice paper studying the extent to which an individual with known traits can be linked to their genome. Authors argue that the practical risk is minimal, except in specific settings where the number of candidate genomes is very small.
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Arslan Zaidi @aazaidi.bsky.social · 02/06/2026
Our preprint on the genetic regulation of mtDNA gene expression in collaboration with @shwetaramdas.bsky.social and @rajivmccoy.bsky.social .
biorxiv.org
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Harald Ringbauer @hringbauer.bsky.social · 01/06/2026
Great to see @annikafreudiger.bsky.social paper published! 🎉 We analyzed how genetic markers are used to estimate relatedness in wild animals - a big field with 2861 relevant publications. 📈🧬 Even in 2026 mainly STRs are used - and we argue for low coverage WGS data and a simple aDNA estimator.
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Arslan Zaidi @aazaidi.bsky.social · 28/05/2026
Happy to present our perspective on how to think about group-differences in genetic risk. With @nicole-kleman.bsky.social , Meng Lin, and Chris Gignoux.
arxiv.org
Tread lightly interpreting group differences in genetic risk
Observed differences in mean phenotypic values across human groups have attracted renewed interest with the rise of large-scale genomic studies and polygenic risk prediction. However, the genetic basi...
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Reposted by Shai Carmi
Nancy Bird @nancybird1.bsky.social · 20/05/2026
Just published our new paper: “The reliability of inferred archaic segments” 🎉🧬💀 www.pivotscipub.com/hpgg/6/2/000... We systematically compare several published methods and our new method "cp-archaic" using simulations and 1000 Genomes data
pivotscipub.com
The reliability of inferred archaic segments
The reliability of inferred archaic segments
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Patrick Turley @paturley.bsky.social · 19/05/2026
Very excited about this preprint that we just posted. It introduces the Genomic-Relatedness Matched Association (GRMA) study. It’s an extension to family-based GWAS that uses extended relatives beyond only siblings in diverse-ancestry data with very little bias. (Link below.)
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Éadaoin Harney @eadaoinharney.bsky.social · 14/05/2026
I'm thrilled to share our new paper out today in @currentbiology.bsky.social! I teamed up with researchers at @harvardmed.bsky.social and the Smithsonian to study another historical American population using the 23andMe genetic database. 🧵 [1/9] Read it here: www.cell.com/current-biol...
cell.com
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Shai Carmi @shaicarmi.bsky.social · 10/05/2026
Nice review paper on the genetics of founder populations. Covers historical research, recent findings, and methods for studying founder populations in large biobanks. By @christacaggiano.bsky.social, @roohy.bsky.social, @eimearekenny.bsky.social www.annualreviews.org/content/jour...
annualreviews.org
Revisiting Founder Populations in an Age of Global Biobanks
Founder populations have played a pivotal role in human genetics, enabling the discovery of causal variants for disease and providing insight into population history and dynamics. The rapid expansion ...
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Adam Auton @adamauton.bsky.social · 07/05/2026
Population geneticists! Come work at 23andMe! New role just posted. 23andme.wd5.myworkdayjobs.com/23/job/Palo-...
23andme.wd5.myworkdayjobs.com
Scientist, Population Genetics
23andMe is looking for a quantitative scientist with extensive experience in population genetics and statistical modeling of human genetics data to join our R&D team. You will leverage your expert...
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Matt Robinson @mrobinso.bsky.social · 04/05/2026
Just sharing our most recent preprint. Would welcome feedback. Sex differences in the genetic basis of human recombination within 190,000 parent-child pairs. www.biorxiv.org/content/10.6...
biorxiv.org
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Stephan Schiffels @stschiff.bsky.social · 05/05/2026
Finally an official publication of Pileupcaller. Please cite. Thanks to @joss-openjournals.bsky.social for the review process and publishing!
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Luane Landau @lulandau.bsky.social · 05/05/2026
1/ New paper out in Nature Communications! We studied the salivary amylase gene, AMY1, in Indigenous Andean populations and found evidence that high AMY1 copy number rapidly increased in frequency, likely through recent positive selection. doi.org/10.1038/s414...
doi.org
Rapid adaptive increase of amylase gene copy number in Indigenous Andeans - Nature Communications
The salivary amylase gene exhibits copy-number variation linked to dietary shifts. Here, the authors describe an adaptive expansion of the amylase gene in Indigenous Andean populations coinciding with...
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bioRxiv Genetics @biorxiv-genetic.bsky.social · 02/05/2026
Highly efficient genotype compression leveraging genealogical relatedness www.biorxiv.org/content/10.64898/20…
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Todd Lencz @toddlencz.bsky.social · 01/05/2026
New preprint! Introducing DIMPLE-GWAS - a new dimensionality-reduction method to capture latent endophenotypes. Applied to pleiotropic brain imaging data in UK Biobank, we developed a new brain atlas composed of 25 core "clusters" Details below and at my #SOBP talk Sat 3pm
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John Greally @greally.bsky.social · 30/04/2026
Nice piece on today’s eugenics for the rich, polygenic risk scores in embryos. This article is unusually strong in its thoughtful discussion of the underlying science, with contributions by @shaicarmi.bsky.social and others. nymag.com/intelligence...
nymag.com
Can You Really Choose Your ‘Best Baby’?
Anxious parents are buying $50,000 genetic tests that might not be worth much of anything.
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Michelle Meyer @michellemeyer.bsky.social · 30/04/2026
🚨New paper! eConsent can promote cost-effectiveness & equity in research, but how does it compare to traditional consent w/r/t informedness? In this RCT, we tested the Sage Bionetworks eConsent developed by @megdoerr.bsky.social & @wilbanks.bsky.social, used by, eg NIH All of Us & Apple ResearchKit.
Screenshots of the eConsent, showing different user design principles.
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Alicia Martin @genetisaur.bsky.social · 29/04/2026
📣 𝐖𝐞’𝐫𝐞 𝐡𝐢𝐫𝐢𝐧𝐠 𝐚 𝐩𝐨𝐬𝐭𝐝𝐨𝐜 𝐢𝐧 𝐩𝐨𝐩𝐮𝐥𝐚𝐭𝐢𝐨𝐧 & 𝐬𝐭𝐚𝐭𝐢𝐬𝐭𝐢𝐜𝐚𝐥 𝐠𝐞𝐧𝐞𝐭𝐢𝐜𝐬! 🌍📈🧬 If you’re finishing a PhD (or know someone who is) and want to work on complex trait biology + 𝑟𝑒𝑎𝑙-𝑤𝑜𝑟𝑙𝑑 𝑖𝑚𝑝𝑎𝑐𝑡, read on 👇
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Shai Carmi @shaicarmi.bsky.social · 28/04/2026
A new preprint! A short case report in forensic genetics. Skeletal remains discovered in a cave in central Israel were thought to match a person of Ashkenazi Jewish origin missing since 1948. The authorities were confident about the identification, but... 1/3 www.biorxiv.org/content/10.6...
biorxiv.org
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Ying Wang @yingwangyw.bsky.social · 23/04/2026
🎉New preprint: Phenome-derived polygenic scores and social determinants jointly shape context-dependent disease risk. We evaluate disease risk along 2 complementary axes: • how genetic liability is represented • the social context in which it is expressed
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Shai Carmi @shaicarmi.bsky.social · 22/04/2026
Very frustrated about scientific censorship. I submitted the abstract below to two conferences: ESHG and ESHRE. It was rejected from both (not even allowed as a poster). Good thing we have social media to bypass censoring.
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